Research Project: Biyoteknolojik veya Kimyasal Yöntemlerle, insülin, imatinib ve monoklonal Antikor Fonksiyonuna Sahip Olan İlaç Etkin Maddelerinin Se ntezlenmesi, Analitik Karakterizasyonları ve Yapısal Analizi
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Contributors
Funders
ID
TB.00513
Authors
Demirci, Hasan
Faculty Member
Publications
X-ray crystallographic and hydrogen deuterium exchange studies confirm alternate kinetic models for homolog insulin monomers
(Public Library Science, 2025) Ayan, Esra; Demirci, Hasan; Ayan, Esra; Türk, Miray; Tatlı, Özge; Bostan, Sevginur; Telek, Elek; Dingiloğlu, Baran; Doğan, B. Züleyha; Alp, Muhammed Ikbal; Katı, Ahmet; Dinler-Doğanay, Gizem; Department of Molecular Biology and Genetics; Yes; College of Sciences
Despite the crucial role of various insulin analogs in achieving satisfactory glycemic control, a comprehensive understanding of their in-solution dynamic mechanisms still holds the potential to further optimize rapid insulin analogs, thus significantly improving the well-being of individuals with Type 1 Diabetes. Here, we employed hydrogen-deuterium exchange mass spectrometry to decipher the molecular dynamics of newly modified and functional insulin analog. A comparative analysis of H/D dynamics demonstrated that the modified insulin exchanges deuterium atoms faster and more extensively than the intact insulin aspart. Additionally, we present new insights derived from our 2.5 Å resolution X-ray crystal structure of modified hexamer insulin analog at ambient temperature. Furthermore, we obtained a distinctive side-chain conformation of the Asn3 residue on the B chain (AsnB3) by operating a comparative analysis with a previously available cryogenic rapid-acting insulin structure (PDB_ID: 4GBN). The experimental conclusions have demonstrated compatibility with modified insulin’s distinct cellular activity, comparably to aspart. Additionally, the hybrid structural approach combined with computational analysis employed in this study provides novel insight into the structural dynamics of newly modified and functional insulin vs insulin aspart monomeric entities. It allows further molecular understanding of intermolecular interrelations driving dissociation kinetics and, therefore, a fast action mechanism.
Experimental and computational insights into the structural dynamics of the Fc fragment of IgG1 subtype from biosimilar VEGF-Trap
(Wiley, 2025) Destan, Ebru; Demirci, Hasan; Destan, Ebru; Turkut, Engin; Aldeniz, Alper; Kang, Jungmin; Tosha, Takehiko; Yabashi, Makina; Yilmaz, Baris; Can Timucin, Ahmet; Matsuura, Hiroaki; Kawano, Yoshiaki; Cinkaya, Irfan; Graduate School of Sciences and Engineering; Department of Molecular Biology and Genetics; KUISCID (Koç University İşbank Center for Infectious Diseases); Yes; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING; College of Sciences; Research Center
The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half-life. A prime example is VEGF-Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)-1 and VEGFR-2. The Fc region's role in N-glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near-physiological temperature structures of the N-glycan-bound Fc fragment of IgG1 subtype from a biosimilar VEGF-Trap are presented, determined using the SPring-8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan-binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N-glycans on protein stability. These findings offer new insights into the molecular basis of Fc-mediated functions and provide valuable information for the design of next-generation therapeutics.
A brief atlas of insulin
(Bentham Science Publishers, 2023) Demirci, Hasan; Ayan, Esra; KUISCID (Koç University İşbank Center for Infectious Diseases); Department of Molecular Biology and Genetics; Yes; College of Sciences; Research Center
Insulin is an essential factor for mammalian organisms: a regulator of glucose metabolism and other key signaling pathways. Insulin is also a multifunctional hormone whose absence can cause many diseases. Recombinant insulin is widely used in the treatment of diabetes. Understanding insulin, biosimilars, and biobetters from a holistic perspective will help pharmacologically user-friendly molecules design and develop personalized medicine-oriented therapeutic strategies for diabetes. Additionally, it helps to understand the underlying mechanism of other insulin-dependent metabolic disorders. The purpose of this atlas is to review insulin from a biotechnological, basic science, and clinical perspective, explain nearly all insulin-related disorders and their underlying molecular mechanisms, explore exogenous/recombinant production strategies of patented and research-level insulin/analogs, and highlight their mechanism of action from a structural perspective. Combined with computational analysis, comparisons of insulin and analogs also provide novel information about the structural dynamics of insulin.
Comparative study of high-resolution LysB29(Nε-myristoyl) des(B30) insulin structures display novel dynamic causal interrelations in monomeric-dimeric motions
(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Demirci, Hasan; Destan, Ebru; Çiftçi, Halil İbrahim; Ayan, Esra; Kepçeoğlu, Abdullah; Kati, Ahmet; KUISCID (Koç University İşbank Center for Infectious Diseases); Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; Yes; College of Sciences; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING; Research Center
The treatment of insulin-dependent diabetes mellitus is characterized by artificial supplementation of pancreatic beta-cell ability to regulate sugar levels in the blood. Even though various insulin analogs are crucial for reasonable glycemic control, understanding the dynamic mechanism of the insulin analogs may help to improve the best-protracted insulin analog to assist people with type 1 diabetes (T1D) to live comfortably while maintaining tight glycemic control. Here, we present the high-resolution crystal structure of NN304, known as insulin detemir, to 1.7 angstrom resolution at cryogenic temperature. We computationally further investigated our crystal structure's monomeric-dimeric conformation and dynamic profile by comparing it with a previously available detemir structure (PDB ID: 1XDA). Our structure (PDB ID: 8HGZ), obtained at elevated pH, provides electrostatically triggered minor movements in the equilibrium between alternate conformational substates compared to the previous structure, suggesting it might induce an intermediate state in the dissociation pathway of the insulin detemir's hexamer:dihexamer equilibrium. Supplemented with orientational cross-correlation analysis by a Gaussian network model (GNM), this alternate oligomeric conformation offers the distinct cooperative motions originated by loose coupling of distant conformational substates of a protracted insulin analog that has not been previously observed.
